Hello researchers,
Is PROCHECK the correct tool to check the stereochemical quality of small peptides? My peptide of interest: polypeptide with 16 alanine residues.
Many thanks,
Neena
Dear Neena,
PROCHECK is ok to check for stereo chemical quality of small peptides, as long as you have got the peptide structure in pdb format. I recommend using one of the online web servers available to avoid spending time installing it.
Best wishes,
Patrick
Dear Neena,
to me it is not clear what you want to do. Do you have NMR data (spectra, chemical shifts, 3D structure calculated...) which you want to use to check for enantionmeric purity of your 16-Ala peptide? My experience tells that it will be nearly impossible to rule out a complete epimersation of one (or several) peptide bonds conclusively. If you have too many NMR signals (side-peaks) their presence will tell you that side-products with wrong stereochemistry are likely, but it still will be very difficult to decide on details of the wrong stereochemistry.
Kind regards
Alfred
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